scholarly journals Alkalibaculum bacchi gen. nov., sp. nov., a CO-oxidizing, ethanol-producing acetogen isolated from livestock-impacted soil

2010 ◽  
Vol 60 (10) ◽  
pp. 2483-2489 ◽  
Author(s):  
Toby D. Allen ◽  
Matthew E. Caldwell ◽  
Paul A. Lawson ◽  
Raymond L. Huhnke ◽  
Ralph S. Tanner
Keyword(s):  
Gene Sequence ◽  
Rrna Gene ◽  
The Novel ◽  
Gram Positive Bacteria ◽  
Phylogenetic Studies ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Optimum Ph ◽  
Novel Genus And Species ◽  
Acetogenic Bacterium

Phenotypic and phylogenetic studies were performed on three strains of an acetogenic bacterium isolated from livestock-impacted soil. The bacterium stained Gram-negative and was a non-spore-forming rod that was motile by peritrichous flagella. The novel strains had an optimum pH for growth of 8.0–8.5 and utilized H2 : CO2, CO : CO2, glucose, fructose, mannose, turanose, ribose, trimethylamine, pyruvate, methanol, ethanol, n-propanol and n-butanol as growth substrates. Acetate was produced from glucose. Acetate, CO2 and ethanol were produced from CO : CO2. 16S rRNA gene sequence analysis indicated that the novel strains formed a new subline in the family Eubacteriaceae (rRNA cluster XV) of the low G+C-containing Gram-positive bacteria of the class Clostridia. The DNA G+C base composition was 34 mol%. Cell wall analysis revealed the existence of a novel B-type peptidoglycan similar to the B2α-type (B4) configuration with a variation containing aspartic acid. Based on phylogenetic and phenotypic evidence, it is proposed that the new isolates represent a novel genus and species, for which the name Alkalibaculum bacchi gen. nov., sp. nov. is proposed. The type strain of the type species is CP11T (=ATCC BAA-1772T=DSM 22112T).

scholarly journals Parapedobacter koreensis gen. nov., sp. nov.

2007 ◽  
Vol 57 (6) ◽  
pp. 1336-1341 ◽  
Author(s):  
Myung Kyum Kim ◽  
Ju-Ryun Na ◽  
Dong Ha Cho ◽  
Nak-Kyun Soung ◽  
Deok-Chun Yang
Keyword(s):  
Gene Sequence ◽  
Sequence Similarity ◽  
Distinct Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Novel Genus And Species ◽  
Physiological And Biochemical

Strain Jip14T, a Gram-negative, non-spore-forming, rod-shaped, non-motile bacterium, was isolated from dried rice straw and characterized in order to determine its taxonomic position. 16S rRNA gene sequence analysis revealed that strain Jip14T belongs to the family Sphingobacteriaceae, and the highest degree of sequence similarity was determined to be to Pedobacter saltans DSM 12145T (88.5 %), Pedobacter africanus DSM 12126T (87.6 %), Pedobacter heparinus DSM 2366T (87.1 %) and Pedobacter caeni LMG 22862T (86.9 %). Chemotaxonomic data revealed that strain Jip14T possesses menaquinone MK-7 and the predominant fatty acids C15 : 0 iso, C16 : 0, C16 : 0 10-methyl, C17 : 0 iso 3-OH and summed feature 3 (C15 : 0 iso 2-OH/C16 : 1 ω7c). The results of physiological and biochemical tests clearly demonstrated that strain Jip14T represents a distinct species. Based on these data, Jip14T should be classified within a novel genus and species, for which the name Parapedobacter koreensis gen. nov., sp. nov. is proposed. The type strain of Parapedobacter koreensis is Jip14T (=KCTC 12643T=LMG 23493T).

scholarly journals Nocardioides ginsengagri sp. nov., isolated from the soil of a ginseng field

2012 ◽  
Vol 62 (Pt_3) ◽  
pp. 591-595 ◽  
Author(s):  
Sang-Hee Lee ◽  
Qing-Mei Liu ◽  
Sung-Taik Lee ◽  
Sun-Chang Kim ◽  
Wan-Taek Im
Keyword(s):  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Novel ◽  
Phenotypic Data ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Bacterium Strain

A Gram-reaction-positive, rod-shaped, non-motile, non-spore-forming bacterium (strain BX5-10T) was isolated from the soil of a ginseng field on Baekdu Mountain in Jilin district, China. The taxonomic position of this bacterium was determined in an investigation based on a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain BX5-10T was shown to belong to the family Nocardioidaceae and to be most closely related to Nocardioides plantarum NCIMB 12834T (96.5 % sequence similarity), Nocardioides dokdonensis KCTC 19309T (96.2 %) and Nocardioides fonticola NAA-13T (95.1 %). Strain BX5-10T was characterized chemotaxonomically as having ll-2,6-diaminopimelic acid in its cell-wall peptidoglycan, MK-8(H4) as the predominant menaquinone and C18 : 1ω9c, C16 : 0 and C17 : 1ω8c as its major fatty acids. The G+C content of the genomic DNA was 70.3 mol%. The novel strain could be differentiated genotypically and phenotypically from all recognized species of the genus Nocardioides. Based on the results of the phylogenetic analyses and the genotypic and phenotypic data, a novel species, Nocardioides ginsengagri sp. nov., is proposed. The type strain is BX5-10T ( = KCTC 19467T = DSM 21362T).

scholarly journals Sphaerisporangium krabiense sp. nov., isolated from soil

2011 ◽  
Vol 61 (12) ◽  
pp. 2890-2894 ◽  
Author(s):  
Chanwit Suriyachadkun ◽  
Suwanee Chunhametha ◽  
Wipaporn Ngaemthao ◽  
Tomohiko Tamura ◽  
Kanyawim Kirtikara ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Aerial Mycelium ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Novel ◽  
Mycolic Acids ◽  
Gram Staining ◽  
Phylogenetic Studies ◽  
Gene Sequence Analysis ◽  
Sequence Similarities

A Gram-staining-positive, filamentous bacterial strain, designated A-T 0308T, was isolated from soil of a tropical mangrove forest in Thailand. Strain A-T 0308T developed spherical sporangia containing non-motile spores on aerial mycelium. The novel strain contained meso-diaminopimelic acid, N-acetyl-type peptidoglycan and madurose, mannose, ribose, galactose and glucose as whole-cell sugars. The predominant menaquinones were MK-9(H4) and MK-9(H6); a small amount of MK-9(H2) and MK-9 was also detected. Mycolic acids were not detected. The diagnostic phospholipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and phosphoglycolipid. The predominant cellular fatty acids were iso-C16 : 0 and 10-methylated C17 : 0. The G+C content of the DNA was 72 mol%. Phenotypic and chemotaxonomic analyses showed that the novel isolate had characteristics typical of members of the genus Sphaerisporangium. 16S rRNA gene sequence analysis also indicated that the strain belongs to the genus Sphaerisporangium and that it represents a clade distinct from other members of the genus with sequence similarities ranging from 96.3 to 97.8 % between the novel strain and its closest relatives. Based on the results of phenotypic, chemotaxonomic and phylogenetic studies, strain A-T 0308T ( = BCC 21702T  = NBRC 107571T) represents a novel species of the genus Sphaerisporangium, for which the name Sphaerisporangium krabiense sp. nov. is proposed.

scholarly journals Laetantesicola Maris Gen. Nov., Sp. Nov. Isolated From the Sea of Japan Shallow Sediments.

2021 ◽  
Author(s):  
Lyudmila A. Romanenko ◽  
Valeriya V. Kurilenko ◽  
Nadezhda Yu. Chernysheva ◽  
Liudmila A. Tekutyeva ◽  
Peter V. Velansky ◽  
...  
Keyword(s):  
Sea Of Japan ◽  
Gene Sequence ◽  
Major Fatty Acid ◽  
The Sea Of Japan ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Novel Genus And Species ◽  
Distinct Lineage

Abstract A Gram-negative, non-motile bacterium КММ 3653T was isolated from a sediment sample from the Sea of Japan seashore, Russia. On the basis of the 16S rRNA gene sequence analysis the strain КММ 3653T was positioned within the family Rhodobacteraceae (class Alphaproteobacteria) forming a distinct lineage with the highest gene sequence similarities to the members of the genera Pacificibacter (95.2-94.7%) and Nioella (95.1-94.5%), respectively. According to the phylogenomic tree based on 400 conserved protein sequences, strain КММ 3653T was placed in the cluster comprising Vannielia litorea, Nioella nitratireducens, Litoreibacter albidus and Pseudoruegeria aquimaris as a separate lineage adjacent to Vannielia litorea KCTC 32083T. The average nucleotide identity values between strain КММ 3653T and Vannielia litorea KCTC 32083T, Nioella nitratireducens KCTC 32417T, Litoreibacter albidus KMM 3851T, and Pseudoruegeria aquimaris CECT 7680T were 71.1, 70.3, 69.6, and 71.0%, respectively. Strain КММ 3653T contained Q-10 as the predominant ubiquinone and C18:1ω7c as the major fatty acid followed by C16:0. The polar lipids were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified phospholipid, two unidentified aminolipids, and five unidentified lipids. The DNA G+C content of 61.8 % was calculated from the genome sequence. Based on the phylogenetic evidence and distinctive phenotypic characteristics, strain КММ 3653T is proposed to be classified as a novel genus and species Laetantesicola maris gen. nov., sp. nov. The type strain of Laetantesicola maris gen. nov., sp. nov. is КММ 3653T (=KCTC 82575T).

scholarly journals Aquitalea magnusonii gen. nov., sp. nov., a novel Gram-negative bacterium isolated from a humic lake

2006 ◽  
Vol 56 (4) ◽  
pp. 867-871 ◽  
Author(s):  
Hoi-Ting Lau ◽  
John Faryna ◽  
Eric W. Triplett
Keyword(s):  
Gene Sequence ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Phylogenetic Distance ◽  
Humic Lake ◽  
Gram Negative ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Novel Genus And Species ◽  
Protein Amino Acids

A Gram-negative, rod-shaped, non-spore-forming betaproteobacterium (TRO-001DR8T) was isolated from humic-lake samples collected from northern Wisconsin, USA. On the basis of 16S rRNA gene sequence analysis, strain TRO-001DR8T belonged to the family Neisseriaceae, and the phylogenetic distance from its closest relative, Chromobacterium violaceum, was 95 %. Strain TRO-001DR8T lacked the violet pigmentation of C. violaceum and shared only 26 % DNA–DNA relatedness with C. violaceum. The DNA G+C content of strain TRO-001DR8T was 59 mol%. The predominant fatty acids were C16 : 1 ω7c + C16 : 1 ω7c 2-OH iso (52·5 %), C16 : 0 (21·7 %), C18 : 1 ω7c (8·0 %) and C12 : 0 (5·1 %). Strain TRO-001DR8T grew optimally at 35 °C and pH 6·0, did not utilize sucrose, but did use glucose, some organic acids and most protein amino acids. Biochemical, physiological, chemotaxonomic and phylogenetic analyses showed that strain TRO-001DR8T could not be assigned to any known genus of the Betaproteobacteria. Therefore, the isolate represents a novel genus and species, for which the name Aquitalea magnusonii gen. nov., sp. nov. is proposed. The type strain is TRO-001DR8T (=ATCC BAA-1216T=BCCM/LMG 23054T).

scholarly journals Salarchaeum japonicum gen. nov., sp. nov., an aerobic, extremely halophilic member of the Archaea isolated from commercial salt

2011 ◽  
Vol 61 (9) ◽  
pp. 2266-2270 ◽  
Author(s):  
Yasuhiro Shimane ◽  
Yuji Hatada ◽  
Hiroaki Minegishi ◽  
Akinobu Echigo ◽  
Syuhei Nagaoka ◽  
...  
Keyword(s):  
New Genus ◽  
Gene Sequence ◽  
Lipid Analysis ◽  
Sequence Similarity ◽  
Maximum Growth ◽  
Rrna Gene ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Optimum Ph ◽  
Extremely Halophilic Archaeon

Strain YSM-79T was isolated from commercial salt made from seawater in Yonaguni island, Okinawa, Japan. The strain is an aerobic, Gram-negative, chemo-organotrophic and extremely halophilic archaeon. Cells are short rods that lyse in distilled water. Growth occurs at 1.5–5.3 M NaCl (optimum 2.5–3.0 M), pH 5.0–8.8 (optimum pH 5.2–6.3) and 20–55 °C (optimum 40 °C). Mg2+ is required for growth, with maximum growth at 200–300 mM Mg2+. Polar lipid analysis revealed the presence of phosphatidylglycerol, phosphatidylglycerophosphate methyl ester, sulfated diglycosyl diether-1 and five unidentified glycolipids. The G+C content of the DNA was 64 mol%. On the basis of 16S rRNA gene sequence analysis, strain YSM-79T was determined to be a member of the family Halobacteriaceae, with the closest related genus being Halobacterium (94 % sequence identity). In addition, the rpoB′ gene sequence of strain YSM-79T had <88 % sequence similarity to those of other members of the family Halobacteriaceae. The results of phenotypic, chemotaxonomic and phylogenetic analysis suggested that strain YSM-79T should be placed in a new genus, Salarchaeum gen. nov., as a representative of Salarchaeum japonicum sp. nov. The type strain is YSM-79T ( = JCM 16327T  = CECT 7563T).

scholarly journals Advenella incenata gen. nov., sp. nov., a novel member of the Alcaligenaceae, isolated from various clinical samples

2005 ◽  
Vol 55 (1) ◽  
pp. 251-256 ◽  
Author(s):  
Tom Coenye ◽  
Elke Vanlaere ◽  
Emly Samyn ◽  
Enevold Falsen ◽  
Peter Larsson ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Random Amplified Polymorphic Dna ◽  
Cell Protein ◽  
Clinical Samples ◽  
Rrna Gene ◽  
The Novel ◽  
Novel Genus ◽  
Gene Sequence Analysis ◽  
The Family

A polyphasic taxonomic study of 14 isolates recovered from various human and veterinary clinical samples was performed. Phenotypically these isolates shared several characteristics with members of the Alcaligenaceae and related genera. Random amplified polymorphic DNA fingerprinting and whole-cell protein analysis suggested the presence of multiple genomic groups, which was confirmed by DNA–DNA hybridization experiments. 16S rRNA gene sequence analysis indicated that these isolates were related to the genera Pelistega, Taylorella, Oligella, Pigmentiphaga, Alcaligenes, Kerstersia, Achromobacter and Bordetella and belonged to the family Alcaligenaceae. Based on the results of the present study the organisms were classified in a novel genus, Advenella gen. nov. This genus comprises one named species, Advenella incenata sp. nov. (type strain LMG 22250T=CCUG 45225T) and five currently unnamed genomic species. The DNA G+C content of members of the novel genus Advenella is between 54·0 and 57·7 mol%.

scholarly journals Aurantivirga profunda gen. nov., sp. nov., isolated from deep-seawater, a novel member of the family Flavobacteriaceae

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4850-4856 ◽  
Author(s):  
Jaeho Song ◽  
Ahyoung Choi ◽  
Mihye Im ◽  
Yochan Joung ◽  
Susumu Yoshizawa ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Deep Seawater ◽  
The Pacific ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Growth Properties ◽  
Novel Genus And Species ◽  
The Pacific Ocean

A Gram-stain-negative, aerobic, proteorhodopsin-containing, orange, rod-shaped bacterium, designated SAORIC-234T, was isolated from deep seawater in the Pacific Ocean. 16S rRNA gene sequence analysis revealed that the strain could be affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes and shared less than 94.6 % similarity with other species of the family with validly published names. The phenotypic characteristics of this novel isolate, such as growth properties and enzyme activities, could be differentiated from those of other species. The strain was non-motile, oxidase-positive and catalase-negative. The G+C content of the genomic DNA was determined to be 34.8 mol% and menaquinone-6 (MK-6) was the predominant isoprenoid quinone. The predominant fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C16 : 0 3-OH, iso-C17 : 0 3-OH and iso-C15 : 0 3-OH. The major polar lipids comprised phosphatidylethanolamine, three unknown aminolipids and three unknown lipids. On the basis of the taxonomic data collected in this study, it was concluded that strain SAORIC-234T represents a novel genus and species in the family Flavobacteriaceae, for which the name Aurantivirga profunda gen. nov., sp. nov. is proposed. The type strain of the type species, Aurantivirga profunda sp. nov., is SAORIC-234T ( = NBRC 110606T = KACC 18400T).

scholarly journals Winogradskyella thalassocola gen. nov., sp. nov., Winogradskyella epiphytica sp. nov. and Winogradskyella eximia sp. nov., marine bacteria of the family Flavobacteriaceae

2005 ◽  
Vol 55 (1) ◽  
pp. 49-55 ◽  
Author(s):  
Olga I. Nedashkovskaya ◽  
Seung Bum Kim ◽  
Suk Kyun Han ◽  
Cindy Snauwaert ◽  
Marc Vancanneyt ◽  
...  
Keyword(s):  
Type Strain ◽  
New Genus ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone ◽  
Peter The Great ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Major Respiratory Quinone

Three novel heterotrophic, Gram-negative, yellow-pigmented, aerobic, gliding, oxidase- and catalase-positive bacteria were isolated from algae collected in the Gulf of Peter the Great, Sea of Japan. 16S rRNA gene sequence analysis revealed that the strains studied represented members of the family Flavobacteriaceae and showed 93·5–93·8 % similarity with their closest relative, Psychroserpens burtonensis. The DNA G+C content of the strains was 34–37 mol%. The major respiratory quinone was MK-6. The predominant fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C15 : 1, iso-C16 : 0-3OH and iso-C17 : 0-3OH. On the basis of their phenotypic, chemotaxonomic, genotypic and phylogenetic characteristics, the newly described bacteria have been assigned to the new genus Winogradskyella gen. nov., as Winogradskyella thalassocola sp. nov. (type strain, KMM 3907T=KCTC 12221T=LMG 22492T=DSM 15363T), Winogradskyella epiphytica sp. nov. (type strain, KMM 3906T=KCTC 12220T=LMG 22491T=CCUG 47091T) and Winogradskyella eximia sp. nov. (type strain, KMM 3944T (=KCTC 12219T=LMG 22474T).

scholarly journals Lysobacter novalis sp. nov., isolated from fallow farmland soil

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 3131-3136 ◽  
Author(s):  
Hina Singh ◽  
Juan Du ◽  
Kyung-Hwa Won ◽  
Jung-Eun Yang ◽  
Shahina Akter ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Gliding Motility ◽  
Rrna Gene ◽  
The Novel ◽  
Respiratory Quinone ◽  
Gene Sequence Analysis ◽  
Farmland Soil ◽  
Major Respiratory Quinone

A novel bacterial strain, designated THG-PC7T, was isolated from fallow farmland soil in Yongin, South Korea. Cells of strain THG-PC7T were Gram-stain-negative, dark yellow, aerobic, rod-shaped and had gliding motility. Strain THG-PC7T grew optimally at 25–35 °C, at pH 7 and in the absence of NaCl. Comparative 16S rRNA gene sequence analysis identified strain THG-PC7T as belonging to the genus Lysobacter, exhibiting highest sequence similarity with Lysobacter ximonensis KCTC 22336T (98.7 %) followed by Lysobacter niastensis KACC 11588T (95.7 %). In DNA–DNA hybridization tests, DNA relatedness between strain THG-PC7T and its closest phylogenetic neighbour L. ximonensis was below 25 %. The DNA G+C content of the novel isolate was determined to be 62.5 mol%. Flexirubin-type pigments were found to be present. The major cellular fatty acids were determined to be iso-C15 : 0, iso-C16 : 0, anteiso-C15 : 0 and iso-C17 : 1ω9c. The major respiratory quinone was identified as ubiquonone-8 (Q8). The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospolipid. On the basis of results from DNA–DNA hybridization and the polyphasic data, strain THG-PC7T represents a novel species of the genus Lysobacter, for which the name Lysobacter novalis sp. nov. is proposed. The type strain is THG-PC7T( = KACC 18276T = CCTCC AB 2014319T).

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